HIV-1 strains are highly variable and this diversity provides a major challenge for vaccine design. A candidate vaccine should provide protection against most clades of HIV. To address this problem, approaches to maximizing immunological strength and breadth are being explored, including strategies that use consensus, center-of-tree or ancestral sequences, multiple strains or mosaic immunogens, immunogens consisting of known epitopes from the database, and chimeric molecules expressing a selection of the most conserved epitopes from different clades of HIV [1-17, 56, 96].
In addition to sequence diversity, the presence of potential immunodominant epitopes provides another hurdle in the development of effective HIV vaccines. Accumulating evidence indicates that immunodominant epitopes exist, and that they may constitute an impediment for the production of effective universal HIV vaccines [18-31], as subdominant epitopes within HIV proteins have generally been associated with virologic control [19,22]. The use of any gene encompassing a complete protein as immunogen contains variable as well as conserved regions. Since variable sequences can mutate to escape immune responses while retaining function, and can contain immunodominant T cell epitopes, we argue that variable segments should be excluded from the design [32]. Our vaccine approach thus focuses on the induction of immune responses to nearly invariable proteome segments, many of which should be essential for the function of the virus, and the prevention of responses against variable segments and potentially immunodominant “decoy” epitopes [32-34].
The conserved element approach is supported by the following observations: (i) Viral proteins recover ancestral amino acid (AA) states when transmitted to a new host [35], and in the absence of the specific immune responses found in the previous host, they can recover a more fit state [36-38]; (ii) changes in conserved AA of viral proteins can destroy or significantly weaken HIV, indicating a critical role in virus biology [39-42]; (iii) CTL responses against specific viral proteins (e.g., Gag) are associated with relative control of viremia [43-50], and in the case of controllers and long-term non-progressors, high avidity CTLs targeting conserved regions have been identified [34, 51]; (iv) immunodominance of some epitopes can obscure or prevent reactivity against other, potentially protective epitopes [52]; (v) some AA segments in viral proteins are conserved throughout a given HIV-1 subtype, the entire group M, and, in some instances, in HIV-2 and SIV [32,53]. Together, these considerations predicted that an HIV vaccine that does not contain variable epitopes, and thus lacks potentially immunodominant decoy epitopes, but instead consists of strictly conserved proteome elements is better fit to induce immune responses able to prevent virus acquisition or virus propagation [32, 53]. The conserved elements used in our work differ from those used by others [11, 12, 16, 17, 54-56] that were selected using different criteria, as we have focused on both conservation and associations of particular sequences with immune control.
Previous work has been performed using Gag as a prototype vaccine, because Gag-specific T cell responses were found to correlate with control of viremia in clade B and C infected individuals [43, 48-50]. Seven highly conserved elements (CE) were identified in HIV-1 p24gag[32, 34] (see also FIG. 1A). Indeed, a cross-sectional ex vivo study showed broad recognition of several CE in the context of wide HLA diversity and identified T cell responses of high functional avidity and broad variant reactivity [34], predominantly in controller individuals, suggesting an association between these T-cell responses and HIV control.
The present invention address the need for an improved protocol for inducing an immune response by providing a strategy based on employing DNA constructs encoding conserve elements in conjunction with constructs encoding the substantially full-length protein from which the conserved element vaccine is derived.